Stem cell therapy is a rapidly advancing field where huge strides have been made in the repair of critical organs. Unfortunately, as with any other graft, stem cell transplants have a high probability of developing immune-mediated complications ultimately resulting in rejection. While strategies such as host immune suppression or use of host-derived cells address the issue of rejection, they are not ideal due to compromised patient health or the prohibitive cost of individualized treatment. Identification of key triggers and development of novel, broadly applicable strategies to specifically control the immune response is imperative for wide scale implementation of cell therapies. Alanyl (membrane) aminopeptidase (ANPEP) is a cell surface protease expressed by monocytes, macrophages, dendritic cells, among many others. The inventors have recently identified ANPEP as a regulator of receptor-mediated antigen uptake and presentation in dendritic cells, an inflammatory adhesion molecule, a regulator of innate immunity, and a regulator of endocytosis, and tested whether ANPEP was involved in immune responses elicited by stem cell transplantation.